Daisy, Rosalina, and Peach are generally only playable in spinoffs. It was a big deal when Peach was playable in 3DW in the first place because she was kept out of the NSMB games for no reason at all for a long time. Samus is legit, but that's just one, and not one of Nintendo's bigger series at that. Obviously having characters playable in spinoffs isn't the same thing, and Nintendo's refusing to even do that with the Zelda series (Triforce Heroes).
I think the reason Link is singled out so often is because Link is really the best major Nintendo character to do this kind of thing with. Every Link is a different person with a different age, backstory, and familial situation anyway, so why not have one of them be a girl? This is different than say making Mario a woman, because every Mario is the same Mario. Every Link ain't the same Link. Plus, Link isn't a gendered name, but rather just a reference to how Link is supposed to represent the player, 50% of which are women.
Why not both?